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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctgtcttgtttgatgtttaagtaactctttttataaacaattgtgcatgcctctacatcacacctaattaaataaataataaataattatgttgtctgttaatttctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATGGATGAACTCTTATCAATAGGACTGTCTAATGCTAAACAG

Basic information

species Vitis vinifera
transcript Vv08s0007g00290.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g00290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g74330.1 (Oryza sativa), 3'ss of exon 2
----gttt---ctgtcttgtttgatgtttaagta-actctttttataaaca-attgtgcatgcctc--tacatcacacctaattaaataaataataaataattatgttgt-ctgttaatttctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATGGATGAACTCTTATCAATAGGACTGTCTAATGCTAAACAG
     |||   |   |     |  | ||    || ||| |  |  | | || |   | ||  || |  | ||   ||||  |||   | | |  |     | | |  ||  | || | | |||    ||    |  ||     ||||||||||||| |||||||||||||| || || |||| ||||||  || | |  || ||  |   ||||||||||
gtttatttgcaccaaccaacctcctattcctatacactgtactagtcaccataccctacactccccacttcacttcaccacattttcttacttgtt--ctactgtactgcgccgtcattctctacagTATGGCGCCACTT---TCTTCTTCAGAGGCCAGCGCATCTGGGAGGCCGTCATGGCTGAACTTCTACCCAAGGGTCTAGCCCGTGCTAAACAG

upper sequence: Vv08s0007g00290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G141873_T03 (Zea mays), 3'ss of exon 4
gtttctgtcttgtttgatgtttaagtaactctttttataaacaattgtgcatgcctctacatcacacctaattaaataaataataa--ataattatgttgtctgttaatttctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATGGATGAACTCTTATCAATAGGACTGTCTAATGCTAAACAG----------
                                         |   | ||| |   |   || || ||    || ||||     |||  ||||  ||  |   | ||    |  | |  ||||||  |||| | ||||||||||||| ||||| |||||||||||||||||| | |||||  ||   |  || ||    ||||||||||||          
---------------------------------------gtctgatttgcttattttc-cagcaaactatgtttaatactaggtaagcataacaattcttattctttgaattcgcg-cagAATGGTACACGATTCTTCTTCAGAGGCCAGCGTATCTGGGAAGCAGTTATGAACGAACTTGTAGTTAAGGGGCTCAGGAATGCTAAACAGGTCATTCCTT

upper sequence: Vv08s0007g00290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G141873_T06 (Zea mays), 3'ss of exon 4
gtttctgtcttgtttgatgtttaagtaactctttttataaacaattgtgcatgcctctacatcacacctaattaaataaataataa--ataattatgttgtctgttaatttctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATGGATGAACTCTTATCAATAGGACTGTCTAATGCTAAACAG
                                         |   | ||| |   |   || || ||    || ||||     |||  ||||  ||  |   | ||    |  | |  ||||||  |||| | ||||||||||||| ||||| |||||||||||||||||| | |||||  ||   |  || ||    ||||||||||||
---------------------------------------gtctgatttgcttattttc-cagcaaactatgtttaatactaggtaagcataacaattcttattctttgaattcgcg-cagAATGGTACACGATTCTTCTTCAGAGGCCAGCGTATCTGGGAAGCAGTTATGAACGAACTTGTAGTTAAGGGGCTCAGGAATGCTAAACAG

upper sequence: Vv08s0007g00290.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G39570.1 (Glycine max), 3'ss of exon 4
gtttctgtcttgtttgatgtttaag--taactctttttataaacaattgtgcatgcctctacatcacacctaattaaataaataataaataattatgttgtctgttaatttctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATGGATGAACTCTTATCAATAGGACTGTCTAATGCTAAACAG
                  | ||| |  | | |  | || |  ||  ||     ||    ||  |   ||  | ||   |  ||  | | |  || | ||     ||| ||| | |   |||  | ||      | ||||||||||| |||  ||| ||||||||  |||||||||||||||||||||  || ||||||||||| || |||
------------------ggttaggattgatttatgttttgcaccgtt-----tgttgttaacttttacacatttgggtttatgttga-tgtttttcttaaa-attattttatatagcaGAGAGGAAGTGGGTTGTTCTTCAGAGGCCAGGTCATATGGGAAGCTATTATGGATGAACTCTTATCAACTGGCCTGTCTAATGCAAAGCAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|32248985|gb|CD714804.1|CD714804
EST:     TCAAGCTGCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAG                         AATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG
genomic: TCAAGCTGCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAGgtttctgtct ... tctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG
EST: gi|32267540|gb|CD716503.1|CD716503
EST:     TCAAGCTGCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAG                         AATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG
genomic: TCAAGCTGCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAGgtttctgtct ... tctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG
EST: gi|161721699|gb|FC070464.1|FC070464
EST:     TCAAGCTTCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAG                         AATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG
genomic: TCAAGCTGCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAGgtttctgtct ... tctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG
EST: gi|161709860|gb|FC058920.1|FC058920
EST:     TCAAGCTTCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAG                         AATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG
genomic: TCAAGCTGCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAGgtttctgtct ... tctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG
EST: gi|161714990|gb|FC062719.1|FC062719
EST:     TCAAGCTGCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAG                         AATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG
genomic: TCAAGCTGCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAGgtttctgtct ... tctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG
EST: gi|161714186|gb|FC062931.1|FC062931
EST:     TCAAGCTTCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAG                         AATGAAACACAACTCTTCTTCAGAGTTCAGCGCATCTGGGAAGCAGTTATG
genomic: TCAAGCTGCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAGgtttctgtct ... tctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG
EST: gi|32269551|gb|CD718710.1|CD718710
EST:     TCAAGCTGCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAG                         AATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG
genomic: TCAAGCTGCGGTATTGTGATGGTGCTTCTTTTGCTGGAAACTCTCAAAAGgtttctgtct ... tctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacctaattaaataaataataaataattatgttgtctgttaatttctgtgatagAATGAAACACAACTCTTCTTCAGAGGTCAGCGCATCTGGGAAGCAGTTATGGATGAACTCTTATCAATAGGACTGTCTAATGCTAAACAG
                                     tgttaat  putative branch site (score: 3)
                                           tttctgt  CT-rich tract
     taattaaataaataat  TA-rich tract